On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

Abstract

The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.

Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae)

“…With next-generation DNA sequencing (NGS) technologies, genome-wide sequence variation has begun to replace one or a few sequence loci for the identification and delimitation of plant species ( Li et al, 2015 ; Coissac et al, 2016 ; Hollingsworth et al, 2016 ). The genome skimming approach, which uses NGS technologies to generate multi-copy and highly repetitive genome components, such as whole plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) clusters via relatively low coverage genome sequencing ( Straub et al, 2012 ), has been increasingly used for species identification and delimitation in recent years ( Nock et al, 2011 ; Kane et al, 2012 ; Dodsworth, 2015 ; Li et al, 2015 ; Ruhsam et al, 2015 ; Firetti et al, 2017 ; Fu et al, 2019 , 2021 ; Ji et al, 2019a , 2020 , 2021 ; Knope et al, 2020 ; Ślipiko et al, 2020 ; Su et al, 2021 ). Compared with restriction-site associated DNA sequencing (RAD-seq; Miller et al, 2007 ; Baird et al, 2008 ), another NSG-based technique that is extensively used to generate genomic data for plant species identification and delimitation (e.g., Wu et al, 2018 ; Donkpegan et al, 2020 ; Ma et al, 2020 ; Zhou et al, 2020 ; Li et al, 2021 ), the promising advantage of using genome skimming for species identification and delimitation is the avoidance of problems encountered with RAD-seq ( Kane et al, 2012 ; Hollingsworth et al, 2016 ), such as only applying to diploids and generating asymmetric data between distinctly related taxa.…”

The complete chloroplast genome of Prunus phaeosticta (Hance) Maxim. (Rosaceae) and its phylogenetic implications

“… 2021 ; NC059022, NC059023, NC059024, NC059025, NC059026, NC059027, Su et al. 2021 ; NC053881, Wang et al. 2021 ).…”

“… 2020 ; Su et al. 2021 ) However, genomic resources of Laurocerasus species are extremely scarce (Zou et al. 2019 ).…”

Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids

“…Combinations of plastid and biparentally inherited nuclear markers, however, often reveal conflicting phylogenetic signals as a first indicator of reticulate relationships. Analyses of single copy-nuclear gene sequences and plastomes can be useful (e.g., in Maddenia [193]).…”